EHV-1 TSS dynamics
Balázs Kakuk
## Error in read.table(file = file, header = header, sep = sep, quote = quote, :
## object 'config' not foundProject info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)
Canonic TSS dynamics
Those reads were counted only, where the 5-prime adapters were “correct” (according to LoRTIA)
Statistics of counts
Difference from mean
Varcoeff
Clustering of samples
## Bootstrap (r = 0.49)... Done.## Bootstrap (r = 0.59)... Done.## Bootstrap (r = 0.7)... Done.## Bootstrap (r = 0.8)... Done.## Bootstrap (r = 0.9)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.09)... Done.## Bootstrap (r = 1.19)... Done.## Bootstrap (r = 1.29)... Done.## Bootstrap (r = 1.39)... Done.
The sample 48h_3 stands out!
Filtering of samples
Clustering of genes into de-novo clusters using hierarchial clustering
Cluster memberships
## Bootstrap (r = 0.5)... Done.## Bootstrap (r = 0.58)... Done.## Bootstrap (r = 0.69)... Done.## Bootstrap (r = 0.77)... Done.## Bootstrap (r = 0.88)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.08)... Done.## Bootstrap (r = 1.19)... Done.## Bootstrap (r = 1.27)... Done.## Bootstrap (r = 1.38)... Done.Optimal number of clusters
Find the optimal number of clusters to cut the tree at and calculate
Clustering statistics: Cluster number: 5
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 2: 1 ORF4 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 3: 1 ORF5 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 4: 1 ORF7 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 5: 1 ORF9 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 6: 1 ORF10 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 7: 1 ORF17 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 8: 1 ORF20 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 9: 1 ORF21 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 10: 1 ORF30 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 11: 1 ORF31 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 12: 1 ORF34 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 13: 1 ORF38 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 14: 1 ORF50 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 15: 1 ORF53 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 16: 1 ORF56 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 17: 1 ORF61 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 18: 1 ORF63 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 19: 1 NOIR_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 20: 1 ORF65_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 21: 1 ORF67_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 22: 1 ORF69 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 23: 1 NOIR_2 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 24: 2 ORF2 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 25: 2 ORF3 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 26: 2 ORF8 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 27: 2 ORF11 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 28: 2 ORF14 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 29: 2 ORF18 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 30: 2 ORF19 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 31: 2 ORF22 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 32: 2 ORF23 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 33: 2 ORF24 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 34: 2 ORF25 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 35: 2 ORF26 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 36: 2 ORF27 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 37: 2 ORF28 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 38: 2 ORF29 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 39: 2 ORF32 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 40: 2 ORF33 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 41: 2 ORF35.5 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 42: 2 ORF36 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 43: 2 ORF37 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 44: 2 ORF39 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 45: 2 CTO 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 46: 2 ORF40 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 47: 2 ORF42 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 48: 2 ORF43 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 49: 2 ORF44 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 50: 2 ORF46 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 51: 2 ORF49 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 52: 2 ORF51 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 53: 2 ORF55 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 54: 2 ORF58 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 55: 2 ORF59 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 56: 2 ORF62 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 57: 2 ORF66_1 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 58: 2 ORF68 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 59: 2 ORF73 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 60: 2 ORF74 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 61: 2 ORF76 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 62: 3 ORF6 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 63: 3 ORF70 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 64: 4 ORF12 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 65: 4 ORF13 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 66: 4 ORF15 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 67: 4 ORF16 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 68: 4 ORF35 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 69: 4 ORF41 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 70: 4 ORF45 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 71: 4 ORF48 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 72: 4 ORF52 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 73: 4 ORF54 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 74: 4 ORF57 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 75: 4 ORF60 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 76: 4 ORF71 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 77: 4 ORF72 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 78: 5 ORF64_1 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 79: 5 ORF75 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004367607 -1.8872285 0.9719524 0.032903167
## 2: 0.004367607 -1.8872285 0.9719524 0.032903167
## 3: 0.004367607 -1.8872285 0.9719524 0.032903167
## 4: 0.004367607 -1.8872285 0.9719524 0.032903167
## 5: 0.004367607 -1.8872285 0.9719524 0.032903167
## 6: 0.004367607 -1.8872285 0.9719524 0.032903167
## 7: 0.004367607 -1.8872285 0.9719524 0.032903167
## 8: 0.004367607 -1.8872285 0.9719524 0.032903167
## 9: 0.004367607 -1.8872285 0.9719524 0.032903167
## 10: 0.004367607 -1.8872285 0.9719524 0.032903167
## 11: 0.004367607 -1.8872285 0.9719524 0.032903167
## 12: 0.004367607 -1.8872285 0.9719524 0.032903167
## 13: 0.004367607 -1.8872285 0.9719524 0.032903167
## 14: 0.004367607 -1.8872285 0.9719524 0.032903167
## 15: 0.004367607 -1.8872285 0.9719524 0.032903167
## 16: 0.004367607 -1.8872285 0.9719524 0.032903167
## 17: 0.004367607 -1.8872285 0.9719524 0.032903167
## 18: 0.004367607 -1.8872285 0.9719524 0.032903167
## 19: 0.004367607 -1.8872285 0.9719524 0.032903167
## 20: 0.004367607 -1.8872285 0.9719524 0.032903167
## 21: 0.004367607 -1.8872285 0.9719524 0.032903167
## 22: 0.004367607 -1.8872285 0.9719524 0.032903167
## 23: 0.004367607 -1.8872285 0.9719524 0.032903167
## 24: 0.005032195 -1.1667586 0.7059510 0.008285088
## 25: 0.005032195 -1.1667586 0.7059510 0.008285088
## 26: 0.005032195 -1.1667586 0.7059510 0.008285088
## 27: 0.005032195 -1.1667586 0.7059510 0.008285088
## 28: 0.005032195 -1.1667586 0.7059510 0.008285088
## 29: 0.005032195 -1.1667586 0.7059510 0.008285088
## 30: 0.005032195 -1.1667586 0.7059510 0.008285088
## 31: 0.005032195 -1.1667586 0.7059510 0.008285088
## 32: 0.005032195 -1.1667586 0.7059510 0.008285088
## 33: 0.005032195 -1.1667586 0.7059510 0.008285088
## 34: 0.005032195 -1.1667586 0.7059510 0.008285088
## 35: 0.005032195 -1.1667586 0.7059510 0.008285088
## 36: 0.005032195 -1.1667586 0.7059510 0.008285088
## 37: 0.005032195 -1.1667586 0.7059510 0.008285088
## 38: 0.005032195 -1.1667586 0.7059510 0.008285088
## 39: 0.005032195 -1.1667586 0.7059510 0.008285088
## 40: 0.005032195 -1.1667586 0.7059510 0.008285088
## 41: 0.005032195 -1.1667586 0.7059510 0.008285088
## 42: 0.005032195 -1.1667586 0.7059510 0.008285088
## 43: 0.005032195 -1.1667586 0.7059510 0.008285088
## 44: 0.005032195 -1.1667586 0.7059510 0.008285088
## 45: 0.005032195 -1.1667586 0.7059510 0.008285088
## 46: 0.005032195 -1.1667586 0.7059510 0.008285088
## 47: 0.005032195 -1.1667586 0.7059510 0.008285088
## 48: 0.005032195 -1.1667586 0.7059510 0.008285088
## 49: 0.005032195 -1.1667586 0.7059510 0.008285088
## 50: 0.005032195 -1.1667586 0.7059510 0.008285088
## 51: 0.005032195 -1.1667586 0.7059510 0.008285088
## 52: 0.005032195 -1.1667586 0.7059510 0.008285088
## 53: 0.005032195 -1.1667586 0.7059510 0.008285088
## 54: 0.005032195 -1.1667586 0.7059510 0.008285088
## 55: 0.005032195 -1.1667586 0.7059510 0.008285088
## 56: 0.005032195 -1.1667586 0.7059510 0.008285088
## 57: 0.005032195 -1.1667586 0.7059510 0.008285088
## 58: 0.005032195 -1.1667586 0.7059510 0.008285088
## 59: 0.005032195 -1.1667586 0.7059510 0.008285088
## 60: 0.005032195 -1.1667586 0.7059510 0.008285088
## 61: 0.005032195 -1.1667586 0.7059510 0.008285088
## 62: 0.004900088 -1.7034767 1.0711351 0.077414527
## 63: 0.004900088 -1.7034767 1.0711351 0.077414527
## 64: 0.004859713 -1.8072219 1.1506135 0.987673767
## 65: 0.004859713 -1.8072219 1.1506135 0.987673767
## 66: 0.004859713 -1.8072219 1.1506135 0.987673767
## 67: 0.004859713 -1.8072219 1.1506135 0.987673767
## 68: 0.004859713 -1.8072219 1.1506135 0.987673767
## 69: 0.004859713 -1.8072219 1.1506135 0.987673767
## 70: 0.004859713 -1.8072219 1.1506135 0.987673767
## 71: 0.004859713 -1.8072219 1.1506135 0.987673767
## 72: 0.004859713 -1.8072219 1.1506135 0.987673767
## 73: 0.004859713 -1.8072219 1.1506135 0.987673767
## 74: 0.004859713 -1.8072219 1.1506135 0.987673767
## 75: 0.004859713 -1.8072219 1.1506135 0.987673767
## 76: 0.004859713 -1.8072219 1.1506135 0.987673767
## 77: 0.004859713 -1.8072219 1.1506135 0.987673767
## 78: 0.004602114 -0.4912168 1.1376079 0.445860724
## 79: 0.004602114 -0.4912168 1.1376079 0.445860724
## se.bp v c pchi
## [1] "ORF67_1" "ORF32" "ORF58" "ORF33" "ORF35.5" "ORF25" "ORF27"
## [8] "ORF62"## [1] 8## [1] "ORF64_1" "ORF75"## [1] 2Clustering statistics: Cluster number: 6
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 2: 1 ORF4 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 3: 1 ORF5 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 4: 1 ORF7 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 5: 1 ORF9 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 6: 1 ORF10 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 7: 1 ORF17 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 8: 1 ORF20 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 9: 1 ORF21 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 10: 1 ORF30 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 11: 1 ORF31 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 12: 1 ORF34 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 13: 1 ORF38 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 14: 1 ORF50 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 15: 1 ORF53 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 16: 1 ORF56 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 17: 1 ORF61 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 18: 1 ORF63 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 19: 1 NOIR_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 20: 1 ORF65_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 21: 1 ORF67_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 22: 1 ORF69 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 23: 1 NOIR_2 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 24: 2 ORF2 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 25: 2 ORF3 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 26: 2 ORF11 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 27: 2 ORF14 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 28: 2 ORF18 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 29: 2 ORF19 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 30: 2 ORF26 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 31: 2 ORF28 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 32: 2 ORF29 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 33: 2 ORF37 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 34: 2 ORF51 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 35: 2 ORF55 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 36: 2 ORF66_1 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 37: 2 ORF73 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 38: 2 ORF76 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 39: 3 ORF6 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 40: 3 ORF70 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 41: 4 ORF8 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 42: 4 ORF22 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 43: 4 ORF23 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 44: 4 ORF24 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 45: 4 ORF25 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 46: 4 ORF27 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 47: 4 ORF32 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 48: 4 ORF33 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 49: 4 ORF35.5 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 50: 4 ORF36 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 51: 4 ORF39 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 52: 4 CTO 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 53: 4 ORF40 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 54: 4 ORF42 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 55: 4 ORF43 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 56: 4 ORF44 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 57: 4 ORF46 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 58: 4 ORF49 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 59: 4 ORF58 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 60: 4 ORF59 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 61: 4 ORF62 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 62: 4 ORF68 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 63: 4 ORF74 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 64: 5 ORF12 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 65: 5 ORF13 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 66: 5 ORF15 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 67: 5 ORF16 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 68: 5 ORF35 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 69: 5 ORF41 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 70: 5 ORF45 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 71: 5 ORF48 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 72: 5 ORF52 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 73: 5 ORF54 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 74: 5 ORF57 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 75: 5 ORF60 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 76: 5 ORF71 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 77: 5 ORF72 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 78: 6 ORF64_1 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 79: 6 ORF75 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004367607 -1.8872285 0.9719524 0.032903167
## 2: 0.004367607 -1.8872285 0.9719524 0.032903167
## 3: 0.004367607 -1.8872285 0.9719524 0.032903167
## 4: 0.004367607 -1.8872285 0.9719524 0.032903167
## 5: 0.004367607 -1.8872285 0.9719524 0.032903167
## 6: 0.004367607 -1.8872285 0.9719524 0.032903167
## 7: 0.004367607 -1.8872285 0.9719524 0.032903167
## 8: 0.004367607 -1.8872285 0.9719524 0.032903167
## 9: 0.004367607 -1.8872285 0.9719524 0.032903167
## 10: 0.004367607 -1.8872285 0.9719524 0.032903167
## 11: 0.004367607 -1.8872285 0.9719524 0.032903167
## 12: 0.004367607 -1.8872285 0.9719524 0.032903167
## 13: 0.004367607 -1.8872285 0.9719524 0.032903167
## 14: 0.004367607 -1.8872285 0.9719524 0.032903167
## 15: 0.004367607 -1.8872285 0.9719524 0.032903167
## 16: 0.004367607 -1.8872285 0.9719524 0.032903167
## 17: 0.004367607 -1.8872285 0.9719524 0.032903167
## 18: 0.004367607 -1.8872285 0.9719524 0.032903167
## 19: 0.004367607 -1.8872285 0.9719524 0.032903167
## 20: 0.004367607 -1.8872285 0.9719524 0.032903167
## 21: 0.004367607 -1.8872285 0.9719524 0.032903167
## 22: 0.004367607 -1.8872285 0.9719524 0.032903167
## 23: 0.004367607 -1.8872285 0.9719524 0.032903167
## 24: 0.005032195 -1.1667586 0.7059510 0.008285088
## 25: 0.005032195 -1.1667586 0.7059510 0.008285088
## 26: 0.005032195 -1.1667586 0.7059510 0.008285088
## 27: 0.005032195 -1.1667586 0.7059510 0.008285088
## 28: 0.005032195 -1.1667586 0.7059510 0.008285088
## 29: 0.005032195 -1.1667586 0.7059510 0.008285088
## 30: 0.005032195 -1.1667586 0.7059510 0.008285088
## 31: 0.005032195 -1.1667586 0.7059510 0.008285088
## 32: 0.005032195 -1.1667586 0.7059510 0.008285088
## 33: 0.005032195 -1.1667586 0.7059510 0.008285088
## 34: 0.005032195 -1.1667586 0.7059510 0.008285088
## 35: 0.005032195 -1.1667586 0.7059510 0.008285088
## 36: 0.005032195 -1.1667586 0.7059510 0.008285088
## 37: 0.005032195 -1.1667586 0.7059510 0.008285088
## 38: 0.005032195 -1.1667586 0.7059510 0.008285088
## 39: 0.004900088 -1.7034767 1.0711351 0.077414527
## 40: 0.004900088 -1.7034767 1.0711351 0.077414527
## 41: 0.004859713 -1.8072219 1.1506135 0.987673767
## 42: 0.004859713 -1.8072219 1.1506135 0.987673767
## 43: 0.004859713 -1.8072219 1.1506135 0.987673767
## 44: 0.004859713 -1.8072219 1.1506135 0.987673767
## 45: 0.004859713 -1.8072219 1.1506135 0.987673767
## 46: 0.004859713 -1.8072219 1.1506135 0.987673767
## 47: 0.004859713 -1.8072219 1.1506135 0.987673767
## 48: 0.004859713 -1.8072219 1.1506135 0.987673767
## 49: 0.004859713 -1.8072219 1.1506135 0.987673767
## 50: 0.004859713 -1.8072219 1.1506135 0.987673767
## 51: 0.004859713 -1.8072219 1.1506135 0.987673767
## 52: 0.004859713 -1.8072219 1.1506135 0.987673767
## 53: 0.004859713 -1.8072219 1.1506135 0.987673767
## 54: 0.004859713 -1.8072219 1.1506135 0.987673767
## 55: 0.004859713 -1.8072219 1.1506135 0.987673767
## 56: 0.004859713 -1.8072219 1.1506135 0.987673767
## 57: 0.004859713 -1.8072219 1.1506135 0.987673767
## 58: 0.004859713 -1.8072219 1.1506135 0.987673767
## 59: 0.004859713 -1.8072219 1.1506135 0.987673767
## 60: 0.004859713 -1.8072219 1.1506135 0.987673767
## 61: 0.004859713 -1.8072219 1.1506135 0.987673767
## 62: 0.004859713 -1.8072219 1.1506135 0.987673767
## 63: 0.004859713 -1.8072219 1.1506135 0.987673767
## 64: 0.004602114 -0.4912168 1.1376079 0.445860724
## 65: 0.004602114 -0.4912168 1.1376079 0.445860724
## 66: 0.004602114 -0.4912168 1.1376079 0.445860724
## 67: 0.004602114 -0.4912168 1.1376079 0.445860724
## 68: 0.004602114 -0.4912168 1.1376079 0.445860724
## 69: 0.004602114 -0.4912168 1.1376079 0.445860724
## 70: 0.004602114 -0.4912168 1.1376079 0.445860724
## 71: 0.004602114 -0.4912168 1.1376079 0.445860724
## 72: 0.004602114 -0.4912168 1.1376079 0.445860724
## 73: 0.004602114 -0.4912168 1.1376079 0.445860724
## 74: 0.004602114 -0.4912168 1.1376079 0.445860724
## 75: 0.004602114 -0.4912168 1.1376079 0.445860724
## 76: 0.004602114 -0.4912168 1.1376079 0.445860724
## 77: 0.004602114 -0.4912168 1.1376079 0.445860724
## 78: 0.005252723 -1.2310691 0.9257357 0.181672372
## 79: 0.005252723 -1.2310691 0.9257357 0.181672372
## se.bp v c pchi
## [1] "ORF67_1" "ORF9" "ORF73" "ORF32" "ORF62" "ORF45"## [1] 6## [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF35" "ORF41" "ORF45" "ORF48" "ORF52"
## [10] "ORF54" "ORF57" "ORF60" "ORF71" "ORF72"## [1] 14Clustering statistics: Cluster number: 7
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 2: 1 ORF4 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 3: 1 ORF5 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 4: 1 ORF7 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 5: 1 ORF9 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 6: 1 ORF10 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 7: 1 ORF17 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 8: 1 ORF20 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 9: 1 ORF21 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 10: 1 ORF30 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 11: 1 ORF31 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 12: 1 ORF34 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 13: 1 ORF38 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 14: 1 ORF50 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 15: 1 ORF53 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 16: 1 ORF56 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 17: 1 ORF61 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 18: 1 ORF63 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 19: 1 NOIR_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 20: 1 ORF65_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 21: 1 ORF67_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 22: 1 ORF69 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 23: 1 NOIR_2 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 24: 2 ORF2 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 25: 2 ORF3 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 26: 2 ORF11 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 27: 2 ORF14 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 28: 2 ORF18 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 29: 2 ORF19 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 30: 2 ORF26 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 31: 2 ORF28 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 32: 2 ORF29 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 33: 2 ORF37 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 34: 2 ORF51 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 35: 2 ORF55 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 36: 2 ORF66_1 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 37: 2 ORF73 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 38: 2 ORF76 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 39: 3 ORF6 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 40: 3 ORF70 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 41: 4 ORF8 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 42: 4 ORF22 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 43: 4 ORF23 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 44: 4 ORF24 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 45: 4 ORF25 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 46: 4 ORF27 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 47: 4 ORF32 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 48: 4 ORF33 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 49: 4 ORF35.5 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 50: 4 ORF36 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 51: 4 ORF39 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 52: 4 CTO 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 53: 4 ORF40 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 54: 4 ORF42 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 55: 4 ORF43 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 56: 4 ORF44 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 57: 4 ORF46 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 58: 4 ORF49 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 59: 4 ORF58 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 60: 4 ORF59 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 61: 4 ORF62 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 62: 4 ORF68 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 63: 4 ORF74 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 64: 5 ORF12 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 65: 5 ORF13 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 66: 5 ORF15 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 67: 5 ORF16 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 68: 5 ORF35 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 69: 5 ORF41 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 70: 5 ORF48 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 71: 5 ORF52 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 72: 5 ORF54 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 73: 5 ORF57 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 74: 5 ORF60 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 75: 5 ORF71 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 76: 5 ORF72 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 77: 6 ORF45 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 78: 7 ORF64_1 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 79: 7 ORF75 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004367607 -1.8872285 0.9719524 0.032903167
## 2: 0.004367607 -1.8872285 0.9719524 0.032903167
## 3: 0.004367607 -1.8872285 0.9719524 0.032903167
## 4: 0.004367607 -1.8872285 0.9719524 0.032903167
## 5: 0.004367607 -1.8872285 0.9719524 0.032903167
## 6: 0.004367607 -1.8872285 0.9719524 0.032903167
## 7: 0.004367607 -1.8872285 0.9719524 0.032903167
## 8: 0.004367607 -1.8872285 0.9719524 0.032903167
## 9: 0.004367607 -1.8872285 0.9719524 0.032903167
## 10: 0.004367607 -1.8872285 0.9719524 0.032903167
## 11: 0.004367607 -1.8872285 0.9719524 0.032903167
## 12: 0.004367607 -1.8872285 0.9719524 0.032903167
## 13: 0.004367607 -1.8872285 0.9719524 0.032903167
## 14: 0.004367607 -1.8872285 0.9719524 0.032903167
## 15: 0.004367607 -1.8872285 0.9719524 0.032903167
## 16: 0.004367607 -1.8872285 0.9719524 0.032903167
## 17: 0.004367607 -1.8872285 0.9719524 0.032903167
## 18: 0.004367607 -1.8872285 0.9719524 0.032903167
## 19: 0.004367607 -1.8872285 0.9719524 0.032903167
## 20: 0.004367607 -1.8872285 0.9719524 0.032903167
## 21: 0.004367607 -1.8872285 0.9719524 0.032903167
## 22: 0.004367607 -1.8872285 0.9719524 0.032903167
## 23: 0.004367607 -1.8872285 0.9719524 0.032903167
## 24: 0.005032195 -1.1667586 0.7059510 0.008285088
## 25: 0.005032195 -1.1667586 0.7059510 0.008285088
## 26: 0.005032195 -1.1667586 0.7059510 0.008285088
## 27: 0.005032195 -1.1667586 0.7059510 0.008285088
## 28: 0.005032195 -1.1667586 0.7059510 0.008285088
## 29: 0.005032195 -1.1667586 0.7059510 0.008285088
## 30: 0.005032195 -1.1667586 0.7059510 0.008285088
## 31: 0.005032195 -1.1667586 0.7059510 0.008285088
## 32: 0.005032195 -1.1667586 0.7059510 0.008285088
## 33: 0.005032195 -1.1667586 0.7059510 0.008285088
## 34: 0.005032195 -1.1667586 0.7059510 0.008285088
## 35: 0.005032195 -1.1667586 0.7059510 0.008285088
## 36: 0.005032195 -1.1667586 0.7059510 0.008285088
## 37: 0.005032195 -1.1667586 0.7059510 0.008285088
## 38: 0.005032195 -1.1667586 0.7059510 0.008285088
## 39: 0.004900088 -1.7034767 1.0711351 0.077414527
## 40: 0.004900088 -1.7034767 1.0711351 0.077414527
## 41: 0.004859713 -1.8072219 1.1506135 0.987673767
## 42: 0.004859713 -1.8072219 1.1506135 0.987673767
## 43: 0.004859713 -1.8072219 1.1506135 0.987673767
## 44: 0.004859713 -1.8072219 1.1506135 0.987673767
## 45: 0.004859713 -1.8072219 1.1506135 0.987673767
## 46: 0.004859713 -1.8072219 1.1506135 0.987673767
## 47: 0.004859713 -1.8072219 1.1506135 0.987673767
## 48: 0.004859713 -1.8072219 1.1506135 0.987673767
## 49: 0.004859713 -1.8072219 1.1506135 0.987673767
## 50: 0.004859713 -1.8072219 1.1506135 0.987673767
## 51: 0.004859713 -1.8072219 1.1506135 0.987673767
## 52: 0.004859713 -1.8072219 1.1506135 0.987673767
## 53: 0.004859713 -1.8072219 1.1506135 0.987673767
## 54: 0.004859713 -1.8072219 1.1506135 0.987673767
## 55: 0.004859713 -1.8072219 1.1506135 0.987673767
## 56: 0.004859713 -1.8072219 1.1506135 0.987673767
## 57: 0.004859713 -1.8072219 1.1506135 0.987673767
## 58: 0.004859713 -1.8072219 1.1506135 0.987673767
## 59: 0.004859713 -1.8072219 1.1506135 0.987673767
## 60: 0.004859713 -1.8072219 1.1506135 0.987673767
## 61: 0.004859713 -1.8072219 1.1506135 0.987673767
## 62: 0.004859713 -1.8072219 1.1506135 0.987673767
## 63: 0.004859713 -1.8072219 1.1506135 0.987673767
## 64: 0.004602114 -0.4912168 1.1376079 0.445860724
## 65: 0.004602114 -0.4912168 1.1376079 0.445860724
## 66: 0.004602114 -0.4912168 1.1376079 0.445860724
## 67: 0.004602114 -0.4912168 1.1376079 0.445860724
## 68: 0.004602114 -0.4912168 1.1376079 0.445860724
## 69: 0.004602114 -0.4912168 1.1376079 0.445860724
## 70: 0.004602114 -0.4912168 1.1376079 0.445860724
## 71: 0.004602114 -0.4912168 1.1376079 0.445860724
## 72: 0.004602114 -0.4912168 1.1376079 0.445860724
## 73: 0.004602114 -0.4912168 1.1376079 0.445860724
## 74: 0.004602114 -0.4912168 1.1376079 0.445860724
## 75: 0.004602114 -0.4912168 1.1376079 0.445860724
## 76: 0.004602114 -0.4912168 1.1376079 0.445860724
## 77: 0.005252723 -1.2310691 0.9257357 0.181672372
## 78: 0.004974133 -1.5296004 0.9769568 0.424389515
## 79: 0.004974133 -1.5296004 0.9769568 0.424389515
## se.bp v c pchi
## [1] "ORF67_1" "ORF9" "ORF73" "ORF27" "ORF32" "ORF62"## [1] 6## [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF35" "ORF41" "ORF48" "ORF52" "ORF54"
## [10] "ORF57" "ORF60" "ORF71" "ORF72"## [1] 13Clustering statistics: Cluster number: 10
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 2: 1 ORF5 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 3: 1 ORF10 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 4: 1 ORF17 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 5: 1 ORF30 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 6: 1 ORF53 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 7: 1 ORF63 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 8: 1 ORF65_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 9: 1 ORF67_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 10: 1 ORF69 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 11: 1 NOIR_2 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 12: 2 ORF2 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 13: 2 ORF3 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 14: 2 ORF11 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 15: 2 ORF14 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 16: 2 ORF18 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 17: 2 ORF19 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 18: 2 ORF26 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 19: 2 ORF29 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 20: 2 ORF37 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 21: 2 ORF51 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 22: 2 ORF55 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 23: 2 ORF66_1 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 24: 2 ORF73 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 25: 2 ORF76 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 26: 3 ORF4 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 27: 3 ORF7 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 28: 3 ORF9 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 29: 3 ORF20 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 30: 3 ORF21 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 31: 3 ORF31 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 32: 3 ORF34 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 33: 3 ORF38 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 34: 3 ORF50 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 35: 3 ORF56 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 36: 3 ORF61 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 37: 3 NOIR_1 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 38: 4 ORF6 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 39: 4 ORF70 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 40: 5 ORF8 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 41: 5 ORF22 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 42: 5 ORF23 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 43: 5 ORF24 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 44: 5 ORF25 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 45: 5 ORF33 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 46: 5 ORF35.5 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 47: 5 ORF36 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 48: 5 ORF39 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 49: 5 CTO 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 50: 5 ORF40 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 51: 5 ORF42 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 52: 5 ORF43 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 53: 5 ORF44 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 54: 5 ORF46 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 55: 5 ORF49 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 56: 5 ORF58 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 57: 5 ORF62 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 58: 5 ORF68 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 59: 5 ORF74 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 60: 6 ORF12 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 61: 6 ORF13 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 62: 6 ORF15 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 63: 6 ORF16 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 64: 6 ORF35 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 65: 6 ORF41 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 66: 6 ORF48 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 67: 6 ORF52 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 68: 6 ORF54 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 69: 6 ORF57 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 70: 6 ORF60 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 71: 6 ORF71 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 72: 6 ORF72 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 73: 7 ORF27 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 74: 7 ORF32 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 75: 7 ORF59 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 76: 8 ORF28 0.8210270 0.9735951 0.4373670 0.022875031 0.0049505146
## 77: 9 ORF45 0.5651379 0.9248487 0.3271761 0.043440538 0.0119522826
## 78: 10 ORF64_1 0.9824929 0.9988394 0.5150579 0.003567073 0.0003270244
## 79: 10 ORF75 0.9824929 0.9988394 0.5150579 0.003567073 0.0003270244
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 2: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 3: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 4: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 5: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 6: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 7: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 8: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 9: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 10: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 11: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 12: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 13: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 14: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 15: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 16: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 17: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 18: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 19: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 20: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 21: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 22: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 23: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 24: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 25: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 26: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 27: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 28: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 29: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 30: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 31: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 32: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 33: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 34: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 35: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 36: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 37: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 38: 0.004859713 -1.8072219 1.1506135 0.9876737674
## 39: 0.004859713 -1.8072219 1.1506135 0.9876737674
## 40: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 41: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 42: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 43: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 44: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 45: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 46: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 47: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 48: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 49: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 50: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 51: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 52: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 53: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 54: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 55: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 56: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 57: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 58: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 59: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 60: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 61: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 62: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 63: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 64: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 65: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 66: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 67: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 68: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 69: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 70: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 71: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 72: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 73: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 74: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 75: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 76: 0.005277089 -0.8894121 1.0470603 0.0007092392
## 77: 0.004937236 -0.4953695 0.9430937 0.2285253818
## 78: 0.005407688 -1.5417408 1.5039873 0.6383969620
## 79: 0.005407688 -1.5417408 1.5039873 0.6383969620
## se.bp v c pchi
## [1] "ORF55" "ORF73" "ORF62" "ORF27" "ORF32" "ORF59"## [1] 6## [1] "ORF8" "ORF22" "ORF23" "ORF24" "ORF25" "ORF33" "ORF35.5"
## [8] "ORF36" "ORF39" "CTO" "ORF40" "ORF42" "ORF43" "ORF44"
## [15] "ORF46" "ORF49" "ORF58" "ORF62" "ORF68" "ORF74" "ORF45"## [1] 21Clustering statistics: Cluster number: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 2: 1 ORF5 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 3: 1 ORF10 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 4: 1 ORF17 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 5: 1 ORF30 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 6: 1 ORF53 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 7: 1 ORF63 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 8: 1 ORF65_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 9: 1 ORF67_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 10: 1 ORF69 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 11: 1 NOIR_2 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 12: 2 ORF2 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 13: 2 ORF3 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 14: 2 ORF11 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 15: 2 ORF14 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 16: 2 ORF18 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 17: 2 ORF19 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 18: 2 ORF26 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 19: 2 ORF29 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 20: 2 ORF37 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 21: 2 ORF51 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 22: 2 ORF55 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 23: 2 ORF66_1 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 24: 2 ORF73 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 25: 2 ORF76 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 26: 3 ORF4 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 27: 3 ORF9 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 28: 3 ORF20 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 29: 3 ORF21 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 30: 3 ORF31 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 31: 3 ORF34 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 32: 3 ORF38 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 33: 3 ORF50 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 34: 3 ORF61 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 35: 4 ORF6 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 36: 4 ORF70 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 37: 5 ORF7 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 38: 5 ORF56 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 39: 5 NOIR_1 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 40: 6 ORF8 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 41: 6 ORF22 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 42: 6 ORF23 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 43: 6 ORF24 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 44: 6 ORF25 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 45: 6 ORF33 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 46: 6 ORF35.5 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 47: 6 ORF36 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 48: 6 ORF39 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 49: 6 CTO 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 50: 6 ORF40 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 51: 6 ORF42 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 52: 6 ORF43 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 53: 6 ORF44 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 54: 6 ORF46 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 55: 6 ORF49 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 56: 6 ORF58 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 57: 6 ORF62 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 58: 6 ORF68 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 59: 6 ORF74 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 60: 7 ORF12 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 61: 7 ORF13 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 62: 7 ORF15 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 63: 7 ORF16 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 64: 7 ORF35 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 65: 7 ORF41 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 66: 7 ORF48 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 67: 7 ORF52 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 68: 7 ORF54 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 69: 7 ORF57 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 70: 7 ORF60 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 71: 7 ORF71 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 72: 7 ORF72 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 73: 8 ORF27 0.8210270 0.9735951 0.4373670 0.022875031 0.0049505146
## 74: 8 ORF59 0.8210270 0.9735951 0.4373670 0.022875031 0.0049505146
## 75: 9 ORF28 0.5651379 0.9248487 0.3271761 0.043440538 0.0119522826
## 76: 10 ORF32 0.9824929 0.9988394 0.5150579 0.003567073 0.0003270244
## 77: 11 ORF45 0.7492275 0.9767156 0.2557177 0.034782397 0.0050850400
## 78: 12 ORF64_1 0.5275231 0.9246028 0.2892245 0.047108368 0.0121954635
## 79: 12 ORF75 0.5275231 0.9246028 0.2892245 0.047108368 0.0121954635
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 2: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 3: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 4: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 5: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 6: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 7: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 8: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 9: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 10: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 11: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 12: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 13: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 14: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 15: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 16: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 17: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 18: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 19: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 20: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 21: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 22: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 23: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 24: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 25: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 26: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 27: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 28: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 29: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 30: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 31: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 32: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 33: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 34: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 35: 0.004859713 -1.8072219 1.1506135 0.9876737674
## 36: 0.004859713 -1.8072219 1.1506135 0.9876737674
## 37: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 38: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 39: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 40: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 41: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 42: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 43: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 44: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 45: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 46: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 47: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 48: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 49: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 50: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 51: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 52: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 53: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 54: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 55: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 56: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 57: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 58: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 59: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 60: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 61: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 62: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 63: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 64: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 65: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 66: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 67: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 68: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 69: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 70: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 71: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 72: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 73: 0.005277089 -0.8894121 1.0470603 0.0007092392
## 74: 0.005277089 -0.8894121 1.0470603 0.0007092392
## 75: 0.004937236 -0.4953695 0.9430937 0.2285253818
## 76: 0.005407688 -1.5417408 1.5039873 0.6383969620
## 77: 0.004595546 -0.6667982 1.3234023 0.9043442194
## 78: 0.004767205 -0.4405398 0.9961916 0.2426264521
## 79: 0.004767205 -0.4405398 0.9961916 0.2426264521
## se.bp v c pchi
## [1] "NOIR_2" "ORF1" "ORF55" "ORF73" "ORF62"## [1] 5## [1] "ORF7" "ORF56" "NOIR_1" "ORF28" "ORF64_1" "ORF75"## [1] 6Selected number of clusters: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 2: 1 ORF5 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 3: 1 ORF10 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 4: 1 ORF17 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 5: 1 ORF30 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 6: 1 ORF53 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 7: 1 ORF63 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 8: 1 ORF65_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 9: 1 ORF67_1 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 10: 1 ORF69 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 11: 1 NOIR_2 0.9871710 0.9978763 0.8199766 0.002829995 0.0005957199
## 12: 2 ORF2 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 13: 2 ORF3 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 14: 2 ORF11 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 15: 2 ORF14 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 16: 2 ORF18 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 17: 2 ORF19 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 18: 2 ORF26 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 19: 2 ORF29 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 20: 2 ORF37 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 21: 2 ORF51 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 22: 2 ORF55 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 23: 2 ORF66_1 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 24: 2 ORF73 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 25: 2 ORF76 0.8727486 0.9694458 0.6775317 0.016844109 0.0054992587
## 26: 3 ORF4 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 27: 3 ORF9 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 28: 3 ORF20 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 29: 3 ORF21 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 30: 3 ORF31 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 31: 3 ORF34 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 32: 3 ORF38 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 33: 3 ORF50 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 34: 3 ORF61 0.9805470 0.9972366 0.7364181 0.003837438 0.0007124588
## 35: 4 ORF6 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 36: 4 ORF70 0.9876023 0.9984510 0.7442836 0.002602583 0.0004231489
## 37: 5 ORF7 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 38: 5 ORF56 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 39: 5 NOIR_1 0.5951566 0.9483249 0.2590130 0.046469616 0.0096061909
## 40: 6 ORF8 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 41: 6 ORF22 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 42: 6 ORF23 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 43: 6 ORF24 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 44: 6 ORF25 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 45: 6 ORF33 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 46: 6 ORF35.5 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 47: 6 ORF36 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 48: 6 ORF39 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 49: 6 CTO 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 50: 6 ORF40 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 51: 6 ORF42 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 52: 6 ORF43 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 53: 6 ORF44 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 54: 6 ORF46 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 55: 6 ORF49 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 56: 6 ORF58 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 57: 6 ORF62 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 58: 6 ORF68 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 59: 6 ORF74 0.9125146 0.9844896 0.6199439 0.012794472 0.0031095485
## 60: 7 ORF12 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 61: 7 ORF13 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 62: 7 ORF15 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 63: 7 ORF16 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 64: 7 ORF35 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 65: 7 ORF41 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 66: 7 ORF48 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 67: 7 ORF52 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 68: 7 ORF54 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 69: 7 ORF57 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 70: 7 ORF60 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 71: 7 ORF71 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 72: 7 ORF72 0.9628981 0.9939043 0.7097462 0.006476931 0.0014084915
## 73: 8 ORF27 0.8210270 0.9735951 0.4373670 0.022875031 0.0049505146
## 74: 8 ORF59 0.8210270 0.9735951 0.4373670 0.022875031 0.0049505146
## 75: 9 ORF28 0.5651379 0.9248487 0.3271761 0.043440538 0.0119522826
## 76: 10 ORF32 0.9824929 0.9988394 0.5150579 0.003567073 0.0003270244
## 77: 11 ORF45 0.7492275 0.9767156 0.2557177 0.034782397 0.0050850400
## 78: 12 ORF64_1 0.5275231 0.9246028 0.2892245 0.047108368 0.0121954635
## 79: 12 ORF75 0.5275231 0.9246028 0.2892245 0.047108368 0.0121954635
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 2: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 3: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 4: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 5: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 6: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 7: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 8: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 9: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 10: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 11: 0.004367607 -1.8872285 0.9719524 0.0329031670
## 12: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 13: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 14: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 15: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 16: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 17: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 18: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 19: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 20: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 21: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 22: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 23: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 24: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 25: 0.005032195 -1.1667586 0.7059510 0.0082850878
## 26: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 27: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 28: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 29: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 30: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 31: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 32: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 33: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 34: 0.004900088 -1.7034767 1.0711351 0.0774145268
## 35: 0.004859713 -1.8072219 1.1506135 0.9876737674
## 36: 0.004859713 -1.8072219 1.1506135 0.9876737674
## 37: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 38: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 39: 0.004602114 -0.4912168 1.1376079 0.4458607244
## 40: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 41: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 42: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 43: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 44: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 45: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 46: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 47: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 48: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 49: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 50: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 51: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 52: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 53: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 54: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 55: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 56: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 57: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 58: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 59: 0.005252723 -1.2310691 0.9257357 0.1816723717
## 60: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 61: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 62: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 63: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 64: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 65: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 66: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 67: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 68: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 69: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 70: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 71: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 72: 0.004974133 -1.5296004 0.9769568 0.4243895152
## 73: 0.005277089 -0.8894121 1.0470603 0.0007092392
## 74: 0.005277089 -0.8894121 1.0470603 0.0007092392
## 75: 0.004937236 -0.4953695 0.9430937 0.2285253818
## 76: 0.005407688 -1.5417408 1.5039873 0.6383969620
## 77: 0.004595546 -0.6667982 1.3234023 0.9043442194
## 78: 0.004767205 -0.4405398 0.9961916 0.2426264521
## 79: 0.004767205 -0.4405398 0.9961916 0.2426264521
## se.bp v c pchi
## [1] "NOIR_2" "ORF1" "ORF55" "ORF73" "ORF62"## [1] 5## [1] "ORF7" "ORF56" "NOIR_1" "ORF28" "ORF64_1" "ORF75"## [1] 6Remove genes from clusters ?
## [1] "ORF7" "ORF56" "NOIR_1" "ORF28" "ORF64_1" "ORF75"## [1] 6## No genes were removed from their corresponding clusters.## cluster N
## <int> <int>
## 1: 6 20
## 2: 2 14
## 3: 7 13
## 4: 1 11
## 5: 3 9
## 6: 5 3
## 7: 4 2
## 8: 8 2
## 9: 12 2
## 10: 9 1
## 11: 10 1
## 12: 11 1Merge cluster stats
Assigning genes to clusters
Summarize and melt
Heatmaps
Normalized Expression
Expression delta ~ 6 hpi
Z-score of expression delta ~ 6 hpi
ORF kinetics, according to literature-based kinetic classes
Barplot of mean and SD
Figure 4 REVIEW - Mean and SD with linear connection
Mean and SD with loess function
Mean and SD with linear connection - Figure 4
Each replicate with loess
ORF kinetics, according to de-novo kinetic classes
Mean and SD with linear connection
Figure 5 REVIEW - Mean and SD with linear connection
Compare literature and de novo kinetic classes
NA shows the number of genes where the clustering did not yield an unambiguous result.
Combined Kinetic classes
De Novo Clusters
Literature clusters
